micro-manager/.github/workflows/check-coverage.yml at develop · precice/micro-manager · GitHub

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name: Check test coverage

on:
  push:
    branches:
      - main
      - develop
  pull_request:
    branches:
      - "*"

jobs:
  coverage:
    name: Run test coverage check
    runs-on: ubuntu-latest
    container: precice/precice:nightly
    steps:
      - name: Checkout repository
        uses: actions/checkout@v6
        with:
          path: micro-manager

      - name: Install dependencies
        run: |
          apt-get -qq update
          apt-get -qq install python3-dev python3-venv git pkg-config
          apt-get -qq install wget build-essential

      - name: Load Cache OpenMPI 5
        id: ompi-cache-load
        uses: actions/cache/restore@v5
        with:
          path: ~/openmpi
          key: openmpi-v5-${{ runner.os }}-build

      - name: Build OpenMPI 5
        if: steps.ompi-cache-load.outputs.cache-hit != 'true'
        run: |
          wget https://download.open-mpi.org/release/open-mpi/v5.0/openmpi-5.0.5.tar.gz
          tar -xzf openmpi-5.0.5.tar.gz
          cd openmpi-5.0.5
          mkdir -p ~/openmpi
          ./configure --prefix=$HOME/openmpi
          make -j$(nproc)
          make install

      - name: Save OpenMPI 5 to cache
        if: steps.ompi-cache-load.outputs.cache-hit != 'true'
        uses: actions/cache/save@v5
        with:
          path: ~/openmpi
          key: openmpi-v5-${{ runner.os }}-build

      - name: Configure OpenMPI
        run: |
          cp -r ~/openmpi/* /usr/local/
          ldconfig
          which mpiexec
          mpiexec --version

      - name: Create a virtual environment and install Micro Manager with coverage
        timeout-minutes: 6
        working-directory: micro-manager
        run: |
          python3 -m venv .venv
          . .venv/bin/activate
          pip install coverage
          pip install .[sklearn,snapshot]
          pip uninstall -y pyprecice

      - name: Run serial unit tests with coverage
        working-directory: micro-manager/tests/unit
        env:
          PYTHONPATH: .
        run: |
          . ../../.venv/bin/activate
          python3 -m coverage run --parallel-mode --source=micro_manager -m unittest test_micro_manager
          python3 -m coverage run --parallel-mode --source=micro_manager -m unittest test_micro_simulation_crash_handling
          python3 -m coverage run --parallel-mode --source=micro_manager -m unittest test_adaptivity_serial
          python3 -m coverage run --parallel-mode --source=micro_manager -m unittest test_domain_decomposition
          python3 -m coverage run --parallel-mode --source=micro_manager -m unittest test_interpolation
          python3 -m coverage run --parallel-mode --source=micro_manager -m unittest test_hdf5_functionality
          python3 -m coverage run --parallel-mode --source=micro_manager -m unittest test_snapshot_computation
          python3 -m coverage run --parallel-mode --source=micro_manager -m unittest test_micro_simulation

      - name: Run tasking unit tests with coverage
        working-directory: micro-manager/tests/unit
        env:
          PYTHONPATH: .
          OMPI_ALLOW_RUN_AS_ROOT: "1"
          OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: "1"
        run: |
          . ../../.venv/bin/activate
          python3 -m coverage run --parallel-mode --source=micro_manager -m unittest test_tasking

      - name: Run parallel unit tests with coverage
        working-directory: micro-manager/tests/unit
        run: |
          . ../../.venv/bin/activate
          mpirun -n 2 --allow-run-as-root -x PYTHONPATH=. python3 -m coverage run --parallel-mode --source=micro_manager -m unittest test_adaptivity_parallel
          mpirun -n 2 --allow-run-as-root -x PYTHONPATH=. python3 -m coverage run --parallel-mode --source=micro_manager -m unittest test_load_balancing

      - name: Combine coverage data
        working-directory: micro-manager/tests/unit
        run: |
          . ../../.venv/bin/activate
          python3 -m coverage combine
          python3 -m coverage report --format=total | python3 ../../check_coverage.py